Comparative analysis of the Tribolium genome

Wed, 01/02/2008 - 14:38

Findings:

Phylogenetic tree (unrooted) relating 5 insect and 5 vertebrate species suggests more basal Hymenoptera radiation, rather than commonly believed Coleoptera. The tree was computed using maximum-likelihood method as implemented in PHYML and TREE-PUZZLE (JTT model with a gamma correction using 4 discrete classes, an estimated alpha parameter and proportion of invariable sites) on concatenated 336,069 aa positions extracted with Gblocks from Muscle alignment of 1,150 universal single-copy orthologs identified using our automatic procedure from the official gene sets (Ensembl for vertebrates). The shown values of statistical support were obtained from 500 replicates of bootstrap analyses. The species names are abbreviated from Latin names.

Comparison of gene repertoire of 5 insect and 5 vertebrate genomes
, ranging from the metazoan core genes (dark fraction on the left) to the species-unique sequences (white band). The striped boxes correspond to insect- and vertebrate-specific orthologous genes. ‘N:N:N’ indicates orthologs present in multiple copies in all species (allowing one loss), and ‘Patchy’ indicates ancient orthologs differentially lost in some lineages (requiring at least two insect and two vertebrate genes).

Comparison of gene family size dynamics (see the table below) showed most prominent expansions of MSF small-solute-transporters and nucleases in Tribolium as compared to other insects (honey bee, fruit fly and two mosquitoes).

We are concentrating now on more detail analysis of orthologous gene losses and expansions.
An example of an expansion is a subset of Cytochrome P450 genes thought to be involved in insecticide resistance, having 19 genes in Tribolium.
The preliminary phylogenetic analysis confirms this Tribolium gene expansion and shows that these duplications are not very recent.

DMEL

AGAM

AAED

AMEL

TCAS

TNIG

GGAL

MDOM

MMUS

HSAP

7

2

5

3

19

0

0

1

1

0

Cytochrome P450 genes in insects
(maximum-likelihood majority-rule tree using phyml, in collaboration with David Nelson)

Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.